Jonathan grew up with ten siblings in London, Ontario, where he was born on February 10, 1859. His parents, Francis Goforth and Jane Bates, had immigrated there, after their marriage, from England.

Jonathan's mother made him start reading the Psalms at age five. Soon, he memorized so much no one would listen to him recite it. As a young boy, Jonathan was constantly reading the Bible and had a longing to learn more about God and be one of his children, but it was not until he was eighteen when he finally committed his life to Christ.

Jonathan always had the dream of becoming an accomplished lawyer and politician. He would often practice speeches behind his house and have heated discussions with himself. Until the day when his father-in-law gave him a book to read: The Memoirs of Robert Murray M'Cheyne. This drastically changed his life and through this book God revealed His calling for Jonathan to become a minister. Since that day he became incredibly involved in his church. He taught a Sunday school class and handed out tracks at the door, but he was still unsatisfied and started a Sunday night church service in the rickety, old schoolhouse. He even started family worship every night in his home, which eventually led to his father's salvation. It was not until later when he heard G. L. MacKay preach and give an invitation to become a missionary, did he decide to serve the Lord in China.

Goforth went to Knox College to ready himself for the mission field; college life was not what he expected. Jonathan was cruelly ridiculed and rejected because he was a poor farm boy, and his clothes were considered shabby in comparison with the big city styles. Soon, however his classmates learned and grew to respect this young man who was on fire for the Lord. They admired Jonathan's passion and determination for missions, and when he did not receive a reply form the China Inland Mission, his classmates were the ones who raised the money for him to go to China.

Jonathan met Rosalind Smith, a rich young lady who had been raised in England, at the Toronto Union Mission in 1885. They were married the next year, the same year of Jonathan's graduation. Goforth was ordained by his church with J. Fraser Smith, and in February 1888 the Goforths, and their companion, finally sailed for China. There, they struggled to adapt to the culture and Jonathan had an especially hard time with the Chinese language. Jonathan and Rosalind had eleven children, five of which died as young children or infants. The Goforths had many different techniques of evangelizing; one technique was the "open house" method. Chinese people were interested in their way of life and so, to reach out, the Goforths would give tours through their home. Other missionaries did not approve of this, but the Goforths continued in this practice anyway. They also used the traditional method of plain, old preaching and Jonathan soon became known as the "Flaming Preacher". He would preach to over 25,000 people at a time.

At he break of the century the Boxer Rebellion broke out. The rebellion was to throw all foreigners out of the country; all missionaries had to flee south to escape the country and angry mobs. On their way to the dock, however, they were attacked by a mob and Jonathan was almost beat to death. Nevertheless, with a few more adventures and God's help they escaped.

Jonathan returned as soon as possible the next year and his wife and children joined him in 1902. Five years later Jonathan and Smith took part in a life-changing revival in Korea. Jonathan was enlightened and encouraged by this and his ministries flourished under the influence.

The Goforths became incredibly involved in the ministry and by 1912 eight Chinese pastors had been trained. Just three years later, Jonathan was awarded the Doctorate of Divinity from Knox College.

Sadly enough, Jonathan went completely blind in 1933 and, because of health complications, was forced to return to Canada the next year. Even so, Jonathan did not let his infirmities hinder his work for the Lord. He continued preaching in Canadian churches until the year of his death in 1936, unfortunately his preaching was not accepted in many pulpits.